Questions tagged [trimming]

To cut from the end. Trimming is often done on raw Illumina reads to discard low-quality bases or adapter sequences. Questions related to trimming algorithms, when, how to trim, trimming software.

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When using cutadapt, can I specify an R2 adapter as optional when I have a required R1 adapter?

I'm using cutadapt 3.5 to trim adapters and perform some filtering on paired-end data. Both R1 and R2 sequences have 3' adapters that might be found depending on the sequence length, but R1 also has ...
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1answer
445 views

insert size pre and post trimming

I have a problem here with my rna seq data: Sequencing details: rRNA was removed, followed by cDNA preparation and generation of stranded libraries using the TruSeq Stranded Total RNA Sample Prep Kit. ...
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50 views

Why is cutadapt discarding some paired end reads?

So, I am using cutadapt to remove two primers from some paired end reads. I have 2 files for each sample, i.e. sample_R1.fastq and sample_R2.fastq. I have primer_1 and primer_2 and both of them can be ...
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1answer
52 views

fastq file format unknown

I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I cat the file I get what seem to me to ...
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1answer
54 views

Telling grep to treat N as [ATCG]

Okay so I'm using grep to try and get a preview of some trimming operations that are not going as expected.. Lets say that my sequence in the FastQ file is: ATNGCNATCG What I want to do is.. ...
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38 views

FastqCleaner in R, not recognizing paired-end fastq file?

I've recently downloaded the FastqCLeaner to process paired-end fastq files locally using R (4.0.3). I'm having trouble with the shiny app. It is not uploading my second fastq file, and is repeated ...
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0answers
67 views

FastQC and Trimmomatic in Galaxy?

I am independently working on data retrieved SRA database, paired-end data as separate inputs. The proceedure I followed is, After running FastQC using Galaxy, the majority of the modules have failed....
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1answer
30 views

Trimmomatic trims most of the reverse strand

I have a paired-end data. It is from small part of human genome not a WGS or WES. I use BWA for alignment and do variant calling. Since I had some false positives I wanted to do trimming. I used ...
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185 views

Calculating the trimming parameter when constructing an additive phylogeny

How do you calculate the trimming parameter when constructing an additive phylogeny? I think it has a relationship with the length of the shortest hanging edge, but I can't figure out how this works.
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1answer
269 views

How to run trimmomatic in HPC

Sorry if this has been asked before, I've done a quick search and I don't think there's an easy explanation for me to understand. I'm really new to bioinformatics/RNASEQ analysis, having only taken ...
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1answer
828 views

What are the right parameters to trim a small RNA transcriptome with trimmomatic?

I'm having some problems with finding the right parameters to trim my small RNA Illumina reads (51 nt long) with Trimmomatic. Before trimming, one of the samples (21M reads) looks like this: So for ...
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3answers
248 views

Tools for quality trimming at 5 prime?

I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations? I'm ...
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2answers
876 views

Is there a safe catch-all adapter sequence for trimming?

I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or ...
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2answers
1k views

"Sequence Duplication Levels" module still fails after pre-processing Illumina data

I want to ask about why the sequence duplication levels are high after I trimmed by using Trimmomatic? I am using the following Trimmomatic operations: ...
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1answer
205 views

Demultiplexing and preprocessing for custom single-nucleus Drop-seq data

I am trying to reproduce the preprocessing of paired-end sequencing reads in Lake et al. (ref. 1). First, paired-end reads were filtered out if read 1 had more than four non-T bases in the last ten ...
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3answers
1k views

Why does cutadapt remove low quality bases from the ends of reads only?

I use cutadapt to remove low quality bases from my Illumina reads. The algorithm only removes low quality bases from the end until it reaches a good quality base. If there is a bad quality base beyond ...
7
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1answer
888 views

How to trim adapter sequences from GSE65360 in order to map the reads?

I am trying to map single-cell chromatin accessibility data from doi:10.1038/nature14590, obtained using scATAC-seq, to the reference genome. Example paired-end reads are here. The reads contain ...
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1answer
1k views

FASTQC overrepresented sequences after trimming

I have a set of RNA-seq samples from different experiments (Single and Paired End, depending on the experiment). I ran FASTQC in all the samples and found overrepresented adapter sequences: I removed ...
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4answers
695 views

How can I systematically detect unknown barcode/adapter sequences within a set of samples?

I have often downloaded datasets from the SRA where the authors failed to mention which adapters were trimmed during the processing. Local alignments tend to overcome this obstacle, but it feels a ...